The file .bash_profile runs when the user logs in. The file .bashrc runs each time a terminal window is opened.
At Terminal Window Startup Time: .bashrc checks to see if /etc/bashrc exists and calls it. /etc/bashrc sets the PATH variable, but DOES NOT include $PATH in its new PATH, causing it to overwrite the PATH that was originally set in the user's .bash_profile.
I suggest removing the PATH variable from .bash_profile. Leave a comment in .bash_profile that the PATH variable should be modified in .bashrc.